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Yorodumi- PDB-4jcu: Crystal structure of a 5-carboxymethyl-2-hydroxymuconate isomeras... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jcu | ||||||
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Title | Crystal structure of a 5-carboxymethyl-2-hydroxymuconate isomerase from Deinococcus radiodurans R1 | ||||||
Components | 5-carboxymethyl-2-hydroxymuconate isomerase | ||||||
Keywords | ISOMERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / alpha/beta / Triangular trimer assembly / PROTEIN STRUCTURE INITIATIVE / 5-carboxymethyl-2-hydroxymuconate | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Al Obaidi, N. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a 5-carboxymethyl-2-hydroxymuconate isomerase from Deinococcus radiodurans R1 Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jcu.cif.gz | 86.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jcu.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 4jcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/4jcu ftp://data.pdbj.org/pub/pdb/validation_reports/jc/4jcu | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17071.732 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: R1 / Gene: DR_A0227 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RYT1 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2M Ammonium acetate, 0.1M Sodium acetate, 25% PEG 4000, 5% Trimethylamine N-oxide dihydrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2013 / Details: Mirrors |
Radiation | Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 21677 / Num. obs: 21677 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.4→2.47 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2 / Num. unique all: 1749 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→45.46 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.082 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.319 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.276 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→45.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.398→2.46 Å / Total num. of bins used: 20
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